Metal Preference Hierarchy in the HDAC8 Active Site: A DFT Study.

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Histone deacetylase 8 (HDAC8) is implicated in various human diseases.
• HDAC8 is a Zn²⁺-dependent metalloenzyme, but its interaction with other metal ions is poorly understood.
• Understanding metal ion selectivity is crucial for HDAC8 inhibitor design.

Purpose of the Study:

• To investigate the binding affinities of biologically relevant metal ions (Fe²⁺, Ni²⁺, Co²⁺, Mg²⁺) for the HDAC8 active site.
• To elucidate the mechanism of metal ion competition with Zn²⁺.
• To establish the intrinsic metal preference hierarchy of HDAC8.

Main Methods:

• Density Functional Theory (DFT) calculations at the B3LYP/6-31+G(d) level.
• Polarizable Continuum Model (PCM) computations in aqueous and methanolic solutions.
• Thermodynamic analysis of metal ion substitution reactions.

Main Results:

• Zn²⁺ is consistently the thermodynamically preferred cofactor for HDAC8.
• Fe²⁺ and Co²⁺ show limited stabilization but are outcompeted by Zn²⁺ due to entropic and desolvation penalties.
• Ni²⁺ and Mg²⁺ exhibit unfavorable binding, with Mg²⁺ strongly excluded.
• Established metal preference hierarchy: Zn²⁺ > Co²⁺ ≈ Fe²⁺ > Ni²⁺ > Mg²⁺.

Conclusions:

• HDAC8 exhibits intrinsic selectivity for Zn²⁺ over other tested metal ions.
• The findings clarify HDAC8 metallo-regulation mechanisms.
• Provides a molecular basis for designing targeted HDAC8 inhibitors.